It said civilian officials provided funding and weapons to pro-Indonesian militias in order to intimidate, threaten and force people to vote for integration with Indonesia.

"Viewed as a whole, the gross human rights violations committed against pro-independence supporters in East Timor in 1999 constitute an organised campaign of violence," the report's authors say in their conclusion.

"The commission recommends that the two presidents together acknowledge responsibility for past violence and apologise to the people of the two nations and especially to the victims of violence for the suffering they have endured."

The report also pointedly recommends that there be no amnesty given to the perpetrators of the violence.

"The commission concludes that amnesty would not be in accordance with its goals of restoring human dignity... Therefore, the commission does not make any recommendations for amnesty," it said.

Abuses acknowledged

Al Jazeera's Marga Ortigas, reporting from East Timor, said many in East Timor had expected a whitewash, but the report uses much stronger language than had been anticipated.

She said the report was a clear acknowledgement that abuses occurred, but questions remain over what will happen next.

The commission itself has no power to prosecute individuals and there is speculation the Indonesian and East Timorese presidents will accept the report but not follow up with any prosecutions for the sake of maintaining friendly relations.

East Timor was formally declared independent in 2002, but in the subsequent six years it has been wracked by political instability and remains one of the poorest countries in Asia.

Earlier this year the country's president and prime minister both survived an assassination attempt.

Given its internal problems and its tiny size compared to Indonesia, East Timor's leaders have generally been wary of raising the issue of the 1999 bloodshed for fear of upsetting Jakarta.

Nonetheless human rights groups have said they will continue to push for the trial of alleged leaders of the violence, including the former head of the Indonesian armed forces, General Wiranto.

Wiranto, who was in charge of security at the time of the independence vote, has denied any wrongdoing.